Gilgamesh is fought as the end boss to The Clash on Big Bridge mission. The battle concludes the mission even if the player loses. He appears as an optional boss with his traditional eight-armed appearance after beating the game twice and completing the second side-history missions. After the mission "The Last Queen Returns to Oblivion", the door to the Rift will open if the player completes all training missions to unlock map areas. The door will appear in four locations: Black Tortoise Crevasse, Militesi Empire near the capital, the Kingdom of Concordia near the Royal Palace and east Rubrum; the locations repeat in this order if the player fights and defeats Gilgamesh. Hence True Gilgamesh has a chance of appearing in one location in each of the four Crystal states.

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Gilgamesh is at LV65 and powerful. He uses a spinning attack where he uses his enormous sword to strike those close to him. When nearby, he can grab a cadet by their neck and then strike with his sword. He moves fairly slowly, but he has a lot of HP.

It is possible to take Gilgamesh on even if he is on a much higher level than the player by exploiting the Breaksight strike chances that trigger when he is about to start an attack. On the last few HP bars the player can deal Breaksight strike many times in a row, quickly depleting his HP. It is best to use a ranged cadet and stay out of his way. Breaksight strike stops Gilgamesh in his tracks briefly.

Gilgamesh is fought using the same strategy as before but now can only be damaged by Breaksights. His attacks stay the same but since Machina is in l'Cie mode, his attacks don't do too much damage. Healing magic isn't usable in this battle due to Machina being sided with Milites at the time. If you are not good at dodging or predicting his attacks patterns, it is a good idea to buy some Potions and Hi-Potions before the mission. Gilgamesh is not a difficult boss if you were able to defeat him in the previous mission.

Gilgamesh will take a random party member to fight and if the player is defeated, he takes the character's equipped weapon. The reward of defeating the True Gilgamesh is the character's ultimate weapon.